RNA polymerase II
Encyclopedia
RNA polymerase II is an enzyme
found in eukaryotic
cells. It catalyzes the transcription
of DNA
to synthesize precursors of mRNA and most snRNA and microRNA. A 550 kDa
complex of 12 subunits, RNAP II is the most studied type of RNA polymerase
. A wide range of transcription factors are required for it to bind to its promoters and begin transcription
.
core RNA polymerase II was first purified using transcription assays. The purified enzyme has typically 10-12 subunits (12 in humans and yeast) and is incapable of specific promoter recognition. Many subunit-subunit interactions are known.
Computer-generated image of POLR2A gene with colorized subunits: green - RPB1 domain 1, blue - RPB1 domain 2, sand - RPB1 domain 3, light blue - RPB1 domain 4, brown - RPB1 domain 6, and magenta - RPB1 CTD.
s can catalyze up to several million reactions per second. Enzyme rates depend on solution conditions and substrate concentration. Like other enzymes POLR2 has a saturation curve and a maximum velocity (Vmax). It has a Km (substrate concentration required for one-half Vmax) and a kcat (the number of substrate molecules handled by one active site per second). The specificity constant is given by kcat/Km. The theoretical maximum for the specificity constant is the diffusion limit of about 108 to 109 (M−1 s−1), where every collision of the enzyme with its substrate results in catalysis.
The turnover number
for RNA polymerase II is 0.16 s−1 subject to concentration. Bacterial RNA polymerase, a relative of RNA Polymerase II, switches between inactivated and activated states by translocating back and forth along the DNA. Concentrations of [NTP]eq = 10 μM GTP, 10 μM UTP, 5 μM ATP and 2.5 μM CTP, produce a mean elongation rate, turnover number, of ~1 bp (NTP)−1 for bacterial RNAP, a relative of RNA polymerase II.
RNA Polymerase II is inhibited by α-amanitin.
RNA polymerase II that is recruited to the promoters of protein
-coding genes in living cells. It consists of RNA polymerase II, a subset of general transcription factor
s, and regulatory protein
s known as SRB proteins.
Part of the assembly of the holoenzyme is referred to as the preinitiation complex
, because its assembly takes place on the gene
promoter before the initiation of transcription
. The mediator complex
acts as a bridge between RNA polymerase II and the transcription factors.
structure and histone
posttranslational modification
help regulate and record the transcription
of genes
by RNA polymerase II.
This pathway gives examples of regulation at these points of transcription:
Please note that this refers to various stages of the process as regulatory steps. It has not been proven that they are used for regulation, but is very likely they are.
RNA Pol II elongation promoters can be summarised in 3 classes.
(HMTs (Histone MethylTransferases)):
COMPASS§† - (COMplex of Proteins ASsociated with Set1) - Methylates lysine 4 of histone H3.
Set2 - Methylates lysine 36 of histone H3.
(interesting irrelevant example: Dot1*‡ - Methylates lysine 79 of histone H3.)
(Other):
Bre1 - Ubiquinates (adds ubiquitin
to) lysine 123 of histone H2B. Associated with pre-initiation and allowing RNA Pol II binding.
or polypeptide terminated by an amino acid
with a free amine
group (-NH2). The convention for writing peptide sequences is to put the N-terminus on the left and write the sequence from N- to C-terminus. When the protein is translated from messenger RNA, it is created from N-terminus to C-terminus.
The N-terminus is the first part of the protein that exits the ribosome
during protein biosynthesis
. It often contains sequences that act as targeting signals, basically intracellular zip code
s, that allow for the protein to be delivered to its designated location within the cell. The targeting signal is usually cleaved off after successful targeting by a processing peptidase. Some proteins are modified posttranslationally.
or polypeptide is the end of the amino acid
chain terminated by a free carboxyl group (-COOH). The convention for writing peptide sequences is to put the C-terminal end on the right and write the sequence from N- to C-terminus.
Each amino acid has a carboxyl group and an amine
group, and amino acids link to one another to form a chain by a dehydration reaction
by joining the amine group of one amino acid to the carboxyl group of the next. Thus polypeptide chains have an end with an unbound carboxyl group, the C-terminus, and an end with an amine group, the N-terminus
. Proteins are naturally synthesized starting from the N-terminus and ending at the C-terminus.
The C-terminus can contain retention signals for protein sorting. The most common ER retention
signal is the amino acid sequence -KDEL (or -HDEL) at the C-terminus, which keeps the protein in the endoplasmic reticulum
and prevents it from entering the secretory pathway
.
The C-terminus of proteins can be modified posttranslationally
, for example, most commonly by the addition of a lipid
anchor to the C-terminus that allows the protein to be inserted into a membrane without having a transmembrane domain. With Pol II, the C-terminus of RPB1
is appended to form the C-terminal domain (CTD).
typically consists of up to 52 repeats of the sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser. Other proteins often bind the C-terminal domain of RNA polymerase in order to activate polymerase activity. It is the protein domain that is involved in the initiation of DNA transcription, the capping
of the RNA transcript
, and attachment to the spliceosome
for RNA splicing
.
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
found in eukaryotic
Eukaryote
A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...
cells. It catalyzes the transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
of DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
to synthesize precursors of mRNA and most snRNA and microRNA. A 550 kDa
KDA
KDA may refer to:* Karachi Development Authority* Kongsberg Defence & Aerospace* Kotelawala Defence Academy* Kramer Design Associates* Lithium diisopropylamide, KDA is the potassium analogue of lithium diisopropylamideOr kDa may refer to:...
complex of 12 subunits, RNAP II is the most studied type of RNA polymerase
RNA polymerase
RNA polymerase is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses...
. A wide range of transcription factors are required for it to bind to its promoters and begin transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
.
Subunits
The eukaryoticEukaryote
A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...
core RNA polymerase II was first purified using transcription assays. The purified enzyme has typically 10-12 subunits (12 in humans and yeast) and is incapable of specific promoter recognition. Many subunit-subunit interactions are known.
Computer-generated image of POLR2A gene with colorized subunits: green - RPB1 domain 1, blue - RPB1 domain 2, sand - RPB1 domain 3, light blue - RPB1 domain 4, brown - RPB1 domain 6, and magenta - RPB1 CTD.
- DNA-directed RNA polymerase II subunit RPB1 - an enzymeEnzymeEnzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
that in humanHumanHumans are the only living species in the Homo genus...
s is encoded by the POLR2APOLR2ADNA-directed RNA polymerase II subunit RPB1 is an enzyme that in humans is encoded by the POLR2A gene.-Interactions:POLR2A has been shown to interact with Transcription elongation regulator 1, CREB-binding protein, BRCA1, GTF2H4, TATA-binding protein, PCAF, GTF2F1, SUPT5H, Transcription Factor II...
geneGeneA gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
. RPB1 is the largest subunit of RNA polymerase II. It contains a carboxy terminal domain (CTD) composed of up to 52 heptapeptide repeats (YSPTSPS) that are essential for polymerase activity. In combination with several other polymerase subunits, it forms the DNA binding domain of the polymerase, a groove in which the DNA template is transcribedTranscription (genetics)Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
into RNA. It strongly interacts with RPB8.
- RPB2 (POLR2BPOLR2BDNA-directed RNA polymerase II subunit RPB2 is an enzyme that in humans is encoded by the POLR2B gene.-Interactions:POLR2B has been shown to interact with POLR2C, POLR2E, POLR2H and POLR2L.-Further reading:...
) - the second-largest subunit that in combination with at least two other polymerase subunits forms a structure within the polymerase that maintains contact in the active site of the enzyme between the DNA template and the newly synthesized RNA.
- RPB3 (POLR2CPOLR2CDNA-directed RNA polymerase II subunit RPB3 is an enzyme that in humans is encoded by the POLR2C gene.-Interactions:POLR2C has been shown to interact with TAF15, POLR2F, POLR2G, POLR2H, POLR2J, POLR2K, POLR2L, ATF4, CCHCR1, POLR2A, POLR2B, POLR2E and Myogenin.-Further reading:...
) - the third-largest subunit. Exists as a heterodimer with another polymerase subunit, POLR2JPOLR2JDNA-directed RNA polymerase II subunit RPB11-a is an enzyme that in humans is encoded by the POLR2J gene.-Interactions:POLR2J has been shown to interact with POLR2C, SATB1 and Apoptosis antagonizing transcription factor.-Further reading:...
forming a core subassembly. RPB3 strongly interacts with RPB1-5, 7, 10-12.
- RNA polymerase II subunit B4RNA polymerase II subunit B4DNA-directed RNA polymerase II subunit RPB4 is an enzyme that in humans is encoded by the POLR2D gene.-Further reading:...
(RPB4) - encoded by the POLR2D geneGeneA gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
is the fourth-largest subunit and may have a stress protective role.
- RPB5 - In humans is encoded by the POLR2EPOLR2EDNA-directed RNA polymerases I, II, and III subunit RPABC1 is a protein that in humans is encoded by the POLR2E gene.-Interactions:POLR2E has been shown to interact with TAF15, POLR2C, POLR2G, POLR2H, POLR2A, POLR2B, POLR2L and GTF2F2....
gene. Two molecules of this subunit are present in each RNA polymerase II. RPB5 strongly interacts with RPB1, RPB3, and RPB6.
- RPB6 (POLR2FPOLR2FDNA-directed RNA polymerases I, II, and III subunit RPABC2 is a protein that in humans is encoded by the POLR2F gene.-Further reading:...
) - forms a structure with at least two other subunits that stabilizes the transcribing polymerase on the DNA template.
- RPB7 - encoded by POLR2GPOLR2GDNA-directed RNA polymerase II subunit RPB7 is an enzyme that in humans is encoded by the POLR2G gene.-Interactions:POLR2G has been shown to interact with TAF15, POLR2C, POLR2H and POLR2E.-Further reading:...
and may play a role in regulating polymerase function. RPB7 interacts strongly with RPB1 and RPB5.
- RPB8 (POLR2HPOLR2HDNA-directed RNA polymerases I, II, and III subunit RPABC3 is a protein that in humans is encoded by the POLR2H gene.-Interactions:POLR2H has been shown to interact with POLR2C, POLR2G, POLR2A, POLR2B and POLR2E.-Further reading:...
) - interacts with subunits RPB1-3, 5, and 7.
- RPB9 - The groove in which the DNA template is transcribed into RNA is composed of RPB9 (POLR2IPOLR2IDNA-directed RNA polymerase II subunit RPB9 is an enzyme that in humans is encoded by the POLR2I gene.-Further reading:...
) and RPB1.
- RPB10 - the product of gene POLR2LPOLR2LDNA-directed RNA polymerases I, II, and III subunit RPABC5 is a protein that in humans is encoded by the POLR2L gene.-Interactions:POLR2L has been shown to interact with POLR2C, POLR2A, POLR2B and POLR2E.-Further reading:...
. It interacts with RPB1-3 and 5, and strongly with RPB3.
- RPB11 - the RPB11 subunit is itself composed of three subunits in humans: POLR2JPOLR2JDNA-directed RNA polymerase II subunit RPB11-a is an enzyme that in humans is encoded by the POLR2J gene.-Interactions:POLR2J has been shown to interact with POLR2C, SATB1 and Apoptosis antagonizing transcription factor.-Further reading:...
(RPB11-a), POLR2J2POLR2J2DNA directed RNA polymerase II polypeptide J-related gene, also known as POLR2J2, is a human gene.-Further reading:...
(RPB11-b), and POLR2J3 (RPB11-c).
- RPB12 - Also interacting with RPB3 is RPB12 (POLR2KPOLR2KDNA-directed RNA polymerases I, II, and III subunit RPABC4 is a protein that in humans is encoded by the POLR2K gene.-Further reading:...
).
Assembly
RPB3 is involved in RNA polymerase II assembly. A subcomplex of RPB2 and RPB3 appears soon after subunit synthesis. This complex subsequently interacts with RPB1. RPB3, RPB5, and RPB7 interact with themselves to form homodimers, and RPB3 and RPB5 together are able to contact all of the other RPB subunits, except RPB9. Only RPB1 strongly binds to RPB5. The RPB1 subunit also contacts RPB7, RPB10, and more weakly but most efficiently with RPB8. Once RPB1 enters the complex, other subunits such as RPB5 and RPB7 can enter, where RPB5 binds to RPB6 and RPB8 and RPB3 brings in RPB10, RPB 11, and RPB12. RPB4 and RPB9 may enter once most of the complex is assembled. RPB4 forms a complex with RPB7.Kinetics
EnzymeEnzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
s can catalyze up to several million reactions per second. Enzyme rates depend on solution conditions and substrate concentration. Like other enzymes POLR2 has a saturation curve and a maximum velocity (Vmax). It has a Km (substrate concentration required for one-half Vmax) and a kcat (the number of substrate molecules handled by one active site per second). The specificity constant is given by kcat/Km. The theoretical maximum for the specificity constant is the diffusion limit of about 108 to 109 (M−1 s−1), where every collision of the enzyme with its substrate results in catalysis.
The turnover number
Turnover number
Turnover number has two related meanings:In enzymology, turnover number is defined as the maximum number of molecules of substrate that an enzyme can convert to product per catalytic site per unit of time and can be calculated as follows: kcat = Vmax/[E]T...
for RNA polymerase II is 0.16 s−1 subject to concentration. Bacterial RNA polymerase, a relative of RNA Polymerase II, switches between inactivated and activated states by translocating back and forth along the DNA. Concentrations of [NTP]eq = 10 μM GTP, 10 μM UTP, 5 μM ATP and 2.5 μM CTP, produce a mean elongation rate, turnover number, of ~1 bp (NTP)−1 for bacterial RNAP, a relative of RNA polymerase II.
RNA Polymerase II is inhibited by α-amanitin.
Holoenzyme
RNA polymerase II holoenzyme is a form of eukaryoticEukaryote
A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...
RNA polymerase II that is recruited to the promoters of protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
-coding genes in living cells. It consists of RNA polymerase II, a subset of general transcription factor
Transcription factor
In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow of genetic information from DNA to mRNA...
s, and regulatory protein
Regulation of gene expression
Gene modulation redirects here. For information on therapeutic regulation of gene expression, see therapeutic gene modulation.Regulation of gene expression includes the processes that cells and viruses use to regulate the way that the information in genes is turned into gene products...
s known as SRB proteins.
Part of the assembly of the holoenzyme is referred to as the preinitiation complex
Preinitiation complex
The preinitiation complex is a large complex of proteins that is necessary for the transcription of protein-coding genes in eukaryotes...
, because its assembly takes place on the gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
promoter before the initiation of transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
. The mediator complex
Mediator (coactivator)
Mediator is a multiprotein complex that functions as a transcriptional coactivator. It was discovered by Roger D. Kornberg, winner of the 2006 Nobel Prize in Chemistry...
acts as a bridge between RNA polymerase II and the transcription factors.
Control by chromatin structure
This is an outline of an example mechanism of yeast cells by which chromatinChromatin
Chromatin is the combination of DNA and proteins that make up the contents of the nucleus of a cell. The primary functions of chromatin are; to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, and to control gene...
structure and histone
Histone
In biology, histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and play a role in gene regulation...
posttranslational modification
Posttranslational modification
Posttranslational modification is the chemical modification of a protein after its translation. It is one of the later steps in protein biosynthesis, and thus gene expression, for many proteins....
help regulate and record the transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
of genes
Gênes
Gênes is the name of a département of the First French Empire in present Italy, named after the city of Genoa. It was formed in 1805, when Napoleon Bonaparte occupied the Republic of Genoa. Its capital was Genoa, and it was divided in the arrondissements of Genoa, Bobbio, Novi Ligure, Tortona and...
by RNA polymerase II.
This pathway gives examples of regulation at these points of transcription:
- Pre-initiation (promotion by Bre1, histone modification)
- Initiation (promotion by TFIIH, Pol II modification AND promotion by COMPASS, histone modification)
- Elongation (promotion by Set2, Histone Modification)
Please note that this refers to various stages of the process as regulatory steps. It has not been proven that they are used for regulation, but is very likely they are.
RNA Pol II elongation promoters can be summarised in 3 classes.
- Drug/sequence-dependent arrest-affected factors (Various interfering proteins)
- Chromatin structure-oriented factors (Histone posttranscriptional modifiers, e.g., HMTs)
- RNA Pol II catalysis-improving factors (Various interfering proteins and Pol II cofactors; see RNA polymerase II).
Protein Complexes Involved
Chromatin structure oriented factors:(HMTs (Histone MethylTransferases)):
COMPASS§† - (COMplex of Proteins ASsociated with Set1) - Methylates lysine 4 of histone H3.
Set2 - Methylates lysine 36 of histone H3.
(interesting irrelevant example: Dot1*‡ - Methylates lysine 79 of histone H3.)
(Other):
Bre1 - Ubiquinates (adds ubiquitin
Ubiquitin
Ubiquitin is a small regulatory protein that has been found in almost all tissues of eukaryotic organisms. Among other functions, it directs protein recycling.Ubiquitin can be attached to proteins and label them for destruction...
to) lysine 123 of histone H2B. Associated with pre-initiation and allowing RNA Pol II binding.
N-terminus
The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) refers to the start of a proteinProtein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
or polypeptide terminated by an amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
with a free amine
Amine
Amines are organic compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are derivatives of ammonia, wherein one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group. Important amines include amino acids, biogenic amines,...
group (-NH2). The convention for writing peptide sequences is to put the N-terminus on the left and write the sequence from N- to C-terminus. When the protein is translated from messenger RNA, it is created from N-terminus to C-terminus.
The N-terminus is the first part of the protein that exits the ribosome
Ribosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....
during protein biosynthesis
Protein biosynthesis
Protein biosynthesis is the process in which cells build or manufacture proteins. The term is sometimes used to refer only to protein translation but more often it refers to a multi-step process, beginning with amino acid synthesis and transcription of nuclear DNA into messenger RNA, which is then...
. It often contains sequences that act as targeting signals, basically intracellular zip code
ZIP Code
ZIP codes are a system of postal codes used by the United States Postal Service since 1963. The term ZIP, an acronym for Zone Improvement Plan, is properly written in capital letters and was chosen to suggest that the mail travels more efficiently, and therefore more quickly, when senders use the...
s, that allow for the protein to be delivered to its designated location within the cell. The targeting signal is usually cleaved off after successful targeting by a processing peptidase. Some proteins are modified posttranslationally.
C-terminus
The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal end, or COOH-terminus) of a proteinProtein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
or polypeptide is the end of the amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
chain terminated by a free carboxyl group (-COOH). The convention for writing peptide sequences is to put the C-terminal end on the right and write the sequence from N- to C-terminus.
Each amino acid has a carboxyl group and an amine
Amine
Amines are organic compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are derivatives of ammonia, wherein one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group. Important amines include amino acids, biogenic amines,...
group, and amino acids link to one another to form a chain by a dehydration reaction
Dehydration reaction
In chemistry and the biological sciences, a dehydration reaction is usually defined as a chemical reaction that involves the loss of water from the reacting molecule. Dehydration reactions are a subset of elimination reactions...
by joining the amine group of one amino acid to the carboxyl group of the next. Thus polypeptide chains have an end with an unbound carboxyl group, the C-terminus, and an end with an amine group, the N-terminus
N-terminal end
The N-terminus refers to the start of a protein or polypeptide terminated by an amino acid with a free amine group . The convention for writing peptide sequences is to put the N-terminus on the left and write the sequence from N- to C-terminus...
. Proteins are naturally synthesized starting from the N-terminus and ending at the C-terminus.
The C-terminus can contain retention signals for protein sorting. The most common ER retention
ER retention
ER retention refers to proteins that are retained in the endoplasmic reticulum, or ER, after folding; these are known as ER resident proteins....
signal is the amino acid sequence -KDEL (or -HDEL) at the C-terminus, which keeps the protein in the endoplasmic reticulum
Endoplasmic reticulum
The endoplasmic reticulum is an organelle of cells in eukaryotic organisms that forms an interconnected network of tubules, vesicles, and cisternae...
and prevents it from entering the secretory pathway
Secretory pathway
The secretory pathway is a series of steps a cell uses to move proteins out of the cell; a process known as secretion. The path of a protein destined for secretion has its origins in the rough endoplasmic reticulum, a membrane-bound compartment in the cell...
.
The C-terminus of proteins can be modified posttranslationally
Posttranslational modification
Posttranslational modification is the chemical modification of a protein after its translation. It is one of the later steps in protein biosynthesis, and thus gene expression, for many proteins....
, for example, most commonly by the addition of a lipid
Lipid
Lipids constitute a broad group of naturally occurring molecules that include fats, waxes, sterols, fat-soluble vitamins , monoglycerides, diglycerides, triglycerides, phospholipids, and others...
anchor to the C-terminus that allows the protein to be inserted into a membrane without having a transmembrane domain. With Pol II, the C-terminus of RPB1
POLR2A
DNA-directed RNA polymerase II subunit RPB1 is an enzyme that in humans is encoded by the POLR2A gene.-Interactions:POLR2A has been shown to interact with Transcription elongation regulator 1, CREB-binding protein, BRCA1, GTF2H4, TATA-binding protein, PCAF, GTF2F1, SUPT5H, Transcription Factor II...
is appended to form the C-terminal domain (CTD).
CTD of RNA polymerase
The carboxy-terminal domain of RNA polymerase IIRNA polymerase II
RNA polymerase II is an enzyme found in eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase...
typically consists of up to 52 repeats of the sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser. Other proteins often bind the C-terminal domain of RNA polymerase in order to activate polymerase activity. It is the protein domain that is involved in the initiation of DNA transcription, the capping
5' cap
The 5' cap is a specially altered nucleotide on the 5' end of precursor messenger RNA and some other primary RNA transcripts as found in eukaryotes. The process of 5' capping is vital to creating mature messenger RNA, which is then able to undergo translation...
of the RNA transcript
Messenger RNA
Messenger RNA is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcribed from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes. Here, the nucleic acid polymer is translated into a polymer of amino acids: a protein...
, and attachment to the spliceosome
Spliceosome
A spliceosome is a complex of snRNA and protein subunits that removes introns from a transcribed pre-mRNA segment. This process is generally referred to as splicing.-Composition:...
for RNA splicing
RNA splicing
In molecular biology and genetics, splicing is a modification of an RNA after transcription, in which introns are removed and exons are joined. This is needed for the typical eukaryotic messenger RNA before it can be used to produce a correct protein through translation...
.
See also
- RNA polymerase IRNA polymerase IRNA polymerase I is, in eukaryotes, the enzyme that only transcribes ribosomal RNA , a type of RNA that accounts for over 50% of the total RNA synthesized in a cell....
- RNA polymerase IIIRNA polymerase IIIRNA polymerase III transcribes DNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs. The genes transcribed by RNA Pol III fall in the category of "housekeeping" genes whose expression is required in all cell types and most environmental conditions...
- RNA polymerase II holoenzymeRNA polymerase II holoenzymeRNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein-coding genes in living cells...
- Post-transcriptional modificationPost-transcriptional modificationPost-transcriptional modification is a process in cell biology by which, in eukaryotic cells, primary transcript RNA is converted into mature RNA. A notable example is the conversion of precursor messenger RNA into mature messenger RNA , which includes splicing and occurs prior to protein synthesis...
- Transcription (genetics)Transcription (genetics)Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
- Eukaryotic transcriptionEukaryotic transcriptionEukaryotic transcription is more complex than prokaryotic transcription. For instance, in eukaryotes the genetic material , and therefore transcription, is primarily localized to the nucleus, where it is separated from the cytoplasm by the nuclear membrane...